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Thomas Down, PhD - Publications

Affiliations: 
Gurdon Institute 
Website:
http://www.gurdon.cam.ac.uk/down.html
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C, Harris TW, Kishore R, Lee R, Lomax J, Li Y, et al. WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Research. 44: D774-80. PMID 26578572 DOI: 10.1093/Nar/Gkv1217  0.319
2015 Geihs M, Yan Y, Walter K, Huang J, Memari Y, Min J, Mead D, Hubbard T, Timpson N, Down T, Soranzo N. An interactive genome browser of association results from the UK10K cohorts project. Bioinformatics (Oxford, England). PMID 26315906 DOI: 10.1093/bioinformatics/btv491  0.319
2013 Puszyk W, Down T, Grimwade D, Chomienne C, Oakey RJ, Solomon E, Guidez F. The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells. The Embo Journal. 32: 1941-52. PMID 23727884 DOI: 10.1038/Emboj.2013.118  0.307
2013 Gemma C, Ramagopalan SV, Down TA, Beyan H, Hawa MI, Holland ML, Hurd PJ, Giovannoni G, Leslie RD, Ebers GC, Rakyan VK. Inactive or moderately active human promoters are enriched for inter-individual epialleles. Genome Biology. 14: R43. PMID 23706135 DOI: 10.1186/gb-2013-14-5-r43  0.331
2012 Evans AL, Faial T, Gilchrist MJ, Down T, Vallier L, Pedersen RA, Wardle FC, Smith JC. Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells. Plos One. 7: e33346. PMID 22479388 DOI: 10.1371/Journal.Pone.0033346  0.339
2012 Saied MH, Marzec J, Khalid S, Smith P, Down TA, Rakyan VK, Molloy G, Raghavan M, Debernardi S, Young BD. Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats. Plos One. 7: e33213. PMID 22479372 DOI: 10.1371/Journal.Pone.0033213  0.414
2011 Movassagh M, Choy MK, Knowles DA, Cordeddu L, Haider S, Down T, Siggens L, Vujic A, Simeoni I, Penkett C, Goddard M, Lio P, Bennett MR, Foo RS. Distinct epigenomic features in end-stage failing human hearts. Circulation. 124: 2411-22. PMID 22025602 DOI: 10.1161/Circulationaha.111.040071  0.418
2011 Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nature Reviews. Genetics. 12: 529-41. PMID 21747404 DOI: 10.1038/Nrg3000  0.306
2011 Cheung MS, Down TA, Latorre I, Ahringer J. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Research. 39: e103. PMID 21646344 DOI: 10.1093/nar/gkr425  0.385
2011 Feber A, Wilson GA, Zhang L, Presneau N, Idowu B, Down TA, Rakyan VK, Noon LA, Lloyd AC, Stupka E, Schiza V, Teschendorff AE, Schroth GP, Flanagan A, Beck S. Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Research. 21: 515-24. PMID 21324880 DOI: 10.1101/Gr.109678.110  0.321
2010 Choy MK, Movassagh M, Goh HG, Bennett MR, Down TA, Foo RS. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated. Bmc Genomics. 11: 519. PMID 20875111 DOI: 10.1186/1471-2164-11-519  0.386
2010 Piipari M, Down TA, Saini H, Enright A, Hubbard TJ. iMotifs: an integrated sequence motif visualization and analysis environment. Bioinformatics (Oxford, England). 26: 843-4. PMID 20106815 DOI: 10.1093/bioinformatics/btq026  0.326
2010 Novakovic B, Wong NC, Sibson M, Ng HK, Morley R, Manuelpillai U, Down T, Rakyan VK, Beck S, Hiendleder S, Roberts CT, Craig JM, Saffery R. DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta. The Journal of Biological Chemistry. 285: 9583-93. PMID 20071334 DOI: 10.1074/Jbc.M109.064956  0.346
2010 Saied M, Khaled S, Down T, Marzec J, Smith P, Debernardi S, Young BD. Genome Wide Study of DNA Methylation In AML Blood. 116: 3618-3618. DOI: 10.1182/Blood.V116.21.3618.3618  0.396
2009 Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D. Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level. Genome Research. 19: 994-1005. PMID 19401398 DOI: 10.1101/Gr.089086.108  0.307
2009 Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nature Genetics. 41: 376-81. PMID 19182803 DOI: 10.1038/Ng.322  0.332
2008 Novakovic B, Rakyan V, Ng HK, Manuelpillai U, Dewi C, Wong NC, Morley R, Down T, Beck S, Craig JM, Saffery R. Specific tumour-associated methylation in normal human term placenta and first-trimester cytotrophoblasts. Molecular Human Reproduction. 14: 547-54. PMID 18708652 DOI: 10.1093/Molehr/Gan046  0.357
2008 Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotechnology. 26: 779-85. PMID 18612301 DOI: 10.1038/Nbt1414  0.349
2008 Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research. 18: 1518-29. PMID 18577705 DOI: 10.1101/Gr.077479.108  0.417
2008 Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, et al. Ensembl 2008. Nucleic Acids Research. 36: D707-14. PMID 18000006 DOI: 10.1093/nar/gkm988  0.356
2007 Prli? A, Down TA, Kulesha E, Finn RD, Kähäri A, Hubbard TJ. Integrating sequence and structural biology with DAS. Bmc Bioinformatics. 8: 333. PMID 17850653 DOI: 10.1186/1471-2105-8-333  0.306
2007 Down TA, Bergman CM, Su J, Hubbard TJ. Large-scale discovery of promoter motifs in Drosophila melanogaster. Plos Computational Biology. 3: e7. PMID 17238282 DOI: 10.1371/journal.pcbi.0030007  0.46
2007 Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, et al. Ensembl 2007. Nucleic Acids Research. 35: D610-7. PMID 17148474 DOI: 10.1093/nar/gkl996  0.391
2006 Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nature Genetics. 38: 1378-85. PMID 17072317 DOI: 10.1038/Ng1909  0.321
2006 Down TA. Multi-genome biology. Genome Biology. 7: 305. PMID 16522222 DOI: 10.1186/gb-2006-7-2-305  0.309
2006 Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, et al. Ensembl 2006. Nucleic Acids Research. 34: D556-61. PMID 16381931 DOI: 10.1093/nar/gkj133  0.38
2005 Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, ... ... Down T, et al. The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 309: 1559-63. PMID 16141072 DOI: 10.1126/Science.1112014  0.382
2005 Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, et al. Ensembl 2005. Nucleic Acids Research. 33: D447-53. PMID 15608235 DOI: 10.1093/nar/gki138  0.378
2004 Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, et al. An overview of Ensembl. Genome Research. 14: 925-8. PMID 15078858 DOI: 10.1101/Gr.1860604  0.417
2004 Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nature Reviews. Cancer. 4: 177-83. PMID 14993899 DOI: 10.1038/Nrc1299  0.321
2004 Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, et al. Ensembl 2004. Nucleic Acids Research. 32: D468-70. PMID 14681459 DOI: 10.1093/nar/gkh038  0.385
2003 Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, et al. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Research. 31: 38-42. PMID 12519943 DOI: 10.1093/Nar/Gkg083  0.444
2002 Down TA, Hubbard TJ. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Research. 12: 458-61. PMID 11875034 DOI: 10.1101/gr.216102  0.306
2002 Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, et al. The Ensembl genome database project. Nucleic Acids Research. 30: 38-41. PMID 11752248 DOI: 10.1093/Nar/30.1.38  0.395
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